Fixed some bugs in create_filehandle() and get_newline() that allow them to play better with STDIN and FileHandle objects. Note that the -file argument to create_filehandle should be either a FileHandle ref or \*STDIN. Any Glob that is passed in is now assumed to be STDIN.

Okay, I fixed create_filehandle() so it doesn't always assume a Glob ref is STDIN.

Fixed various bugs in EMBL parsing and writing. Added support for features which run off the sequence (< and > locations) and zero-width features. Fixed species support in embl.pm

Bio::SeqIO::EMBL

Reorganization of Bio::SeqIO modules

Bio::SeqIO::FTHelper

Added seqio files

Added new files

AUTOLOAD and Exporter cleanup

Fixed various bugs in EMBL parsing and writing. Added support for features which run off the sequence (< and > locations) and zero-width features. Fixed species support in embl.pm

Bio::SeqIO::Fasta

Reorganization of Bio::SeqIO modules

Bio::SeqIO::GCG

Reorganization of Bio::SeqIO modules

Bio::SeqIO::GenBank

Simple module for extraction of sequence/ id/ description/ type from GenBank formatted sequences. nextseq still gobbles up all the sequences it can find in a multiple entry GenBank file. This is definitely alpha at the moment.

Made it so IO is abstracted to the _print and _readline functions so that streams can be tie-ed rather than just files handles

Bio::SeqIO::pir

Reorganization of Bio::SeqIO modules

- write_seq() was calling Seq::names(). Removed this call since names are no longer stored in the Seq. - Fixed redeclaration of my $seq in next_seq().

Bio::SeqIO::raw

Reorganization of Bio::SeqIO modules

Made more jitterbug fixes

Bio::SeqIO::scf

Reorganization of Bio::SeqIO modules

- Removed new() so it will use the inherited new() from SeqIO. (Also, there was a bug in the unshift call in the old new()).

Bio::SeqIO::swiss

Added seqio files

- Removed import statement for StreamI. - cleaned up some checks for undefinedness in write_seq(). Also supressing warnings for undefined fields in write_seq(). - Useless use of hash element in void context in _read_FTHelper_swissprot(): $out->field->{$key}; # was this $out->field($key); # I changed to this (what's the purpose?)

AUTOLOAD and Exporter cleanup

Fixed swissprot parsing

Made it so IO is abstracted to the _print and _readline functions so that streams can be tie-ed rather than just files handles